noone@mail.com Analysis of Dieting study 16S data % Fri Sep 7 05:46:18 2018

(1.1.1.4) Taxonomic level: otu of Subset: All samples, no aggregation, no tests, only plots

(1.1.1.4.1) Loading counts and metadata

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(1.1.1.4.2) Data analysis
(1.1.1.4.2.1) Richness and diversity estimates Before count filtering

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Filtering abundance matrix with arguments [ min_mean :10, min_quant_incidence_frac:0.25, min_quant_mean_frac :0.25]. Filtering features

Note that some community richness estimators will not work correctly if provided with abundance-filtered counts

After filtering, left 87 records for 120 features

Wrote counts and metadata for raw counts After final feature filtering to files data/1.1.1.4.2.1-32378e5b444samples.raw.16s.l.otu.count.tsv,data/1.1.1.4.2.1-32378e5b444samples.raw.16s.l.otu.attr.tsv

Wrote counts and metadata for proportions counts After final feature filtering to files data/1.1.1.4.2.1-3234be14d9dsamples.proportions.16s.l.otu.count.tsv,data/1.1.1.4.2.1-3234be14d9dsamples.proportions.16s.l.otu.attr.tsv

(1.1.1.4.2.2) Default transformations for further data analysis

Specific methods can override these and use their own normalization.

Count normalization method for data analysis (unless modified by specific methods) : [ drop.features:List of 1, ..$ :"other", method.args :List of 1, ..$ theta:1, method :"norm.ihs.prop"]

Wrote counts and metadata for raw counts Normalized after default transformations to files data/1.1.1.4.2.2-3234196d035samples.raw.16s.l.otu.count.tsv,data/1.1.1.4.2.2-3234196d035samples.raw.16s.l.otu.attr.tsv

Count normalization method for abundance plots : [ drop.features:List of 1, ..$ :"other", method.args : list(), method :"norm.prop"]

(1.1.1.4.3) Plots of Abundance.

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(1.1.1.4.3) Figure 233. Clustered heatmap of normalized abundance values. Number of cluster splits is determined automatically with method fpc::pamk. Image file: plots/32341ce43f8.svg.

(1.1.1.4.3) G-test of independence between automatic cluster splits and attribute 'Sample.type'. Number of cluster splits is determined automatically with method fpc::pamk.

Log likelihood ratio (G-test) test of independence with Williams' correction: m_a$attr[, main.meta.var] and split
Test statistic X-squared df P value
13.64 8 0.0917

person) (????). morpheus: Interactive heat maps using 'morpheus.js' and 'htmlwidgets'. R package version 0.1.1.1, <URL: https://github.com/cmap/morpheus.R>.

(1.1.1.4.3) Widget 71. Dynamic Morpheus heatmap of normalized abundance values. It is available here through the link only because it can take a while to render for large datasets. This is very customizable. What you will see initially is just a default starting configuration. Explore its menus. Click to see HTML widget file in full window: ./1.1.1.4.3-3231e89fbe2Dynamic.Morpheus.hea.html

Wrote counts and metadata for raw counts Data used for heatmap with added row cluster splits (clustering by abundance profile) to files data/1.1.1.4.3-3237d61e776samples.raw.htmap.count.tsv,data/1.1.1.4.3-3237d61e776samples.raw.htmap.attr.tsv

(1.1.1.4.3) Figure 234. Clustered heatmap of diversity and normalized abundance values. Number of cluster splits is determined automatically with method fpc::pamk. Image file: plots/3231895e722.svg.

(1.1.1.4.3) G-test of independence between automatic cluster splits and attribute 'Sample.type'. Number of cluster splits is determined automatically with method fpc::pamk.

Log likelihood ratio (G-test) test of independence with Williams' correction: m_a$attr[, main.meta.var] and split
Test statistic X-squared df P value
0.2963 1 0.5862

Wrote counts and metadata for raw counts Data used for heatmap with added row cluster splits (clustering by Renyi diversity indices) to files data/1.1.1.4.3-3236105dd4dsamples.raw.htmap.count.tsv,data/1.1.1.4.3-3236105dd4dsamples.raw.htmap.attr.tsv

(1.1.1.4.4) Ordinations,

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